added pre-commit config file

perrin-isir · Jan 2, 2025 · d106bfc · d106bfc
1 parent 9964603
commit d106bfc
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Showing 6 changed files with 72 additions and 36 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,13 @@
+repos:
+-   repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+    - id: black
+      exclude: ^tmp/
+      language_version: python3
+-   repo: https://github.com/PYCQA/flake8
+    rev: 7.0.0
+    hooks:
+    - id: flake8
+      exclude: ^tmp/
+      args: ['--max-line-length=88', '--extend-ignore=E203']
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -1,4 +1,4 @@
-'''# Configuration file for the Sphinx documentation builder.
+"""# Configuration file for the Sphinx documentation builder.
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
@@ -26,13 +26,12 @@
 
 html_theme = 'alabaster'
 html_static_path = ['_static']
-'''
+"""
 
 # Licensed under the BSD 3-Clause License.
 
-import re
 import sys
-from os.path import abspath, dirname, join
+from os.path import abspath
 
 sys.path.insert(0, abspath(".."))
 
@@ -89,15 +88,15 @@
 # The full version, including alpha/beta/rc tags.
 release = ""
 
-''' #Read version info directly from the module's __init__.py
+""" #Read version info directly from the module's __init__.py
 init_path = join(dirname(dirname(str(abspath(__file__)))), "yomix")
 with open(f"{init_path}/__init__.py", "r") as fh:
     for line in fh:
         match = re.match('__version__ = "((\\d.\\d).\\d)[a-z0-9\\-]*".*', line)
         if match is not None:
             release = match.group(1)
             version = match.group(2)
-            break'''
+            break"""
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -135,4 +134,4 @@
 html_theme_options = {}
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "yomixdoc"
+htmlhelp_basename = "yomixdoc"
diff --git a/yomix/__main__.py b/yomix/__main__.py
@@ -181,7 +181,7 @@ def build_figure(embedding_key):
                         obs_numerical,
                         source_rotmatrix_etc,
                         resize_width_input,
-                        bt_slider_range
+                        bt_slider_range,
                     )
 
                     offset_text_feature_color, offset_label = (
@@ -198,7 +198,7 @@ def build_figure(embedding_key):
                             hidden_checkbox_B,
                             resize_width_input_bis,
                             resize_height_input_bis,
-                            bt_slider_range
+                            bt_slider_range,
                         )
                     )
                     offset_label.visible = False
@@ -314,7 +314,7 @@ def build_figure(embedding_key):
                                             resize_height_input, resize_width_input
                                         ),
                                         points_bokeh_plot,
-                                        bt_slider_range
+                                        bt_slider_range,
                                     ),
                                     bokeh.layouts.row(
                                         bokeh.layouts.column(
@@ -356,7 +356,7 @@ def build_figure(embedding_key):
                                             resize_height_input, resize_width_input
                                         ),
                                         points_bokeh_plot,
-                                        bt_slider_range
+                                        bt_slider_range,
                                     ),
                                     bokeh.layouts.row(
                                         bokeh.layouts.column(

diff --git a/yomix/plotting/features.py b/yomix/plotting/features.py
@@ -21,7 +21,7 @@ def color_by_feature_value(
     hidden_checkbox_B,
     resize_w_input,
     resize_h_input,
-    bt_slider_range
+    bt_slider_range,
 ):
     source = points_bokeh_plot.select(dict(name="scatterplot"))[0].data_source
 
@@ -32,7 +32,9 @@ def color_by_feature_value(
     for i, featname in enumerate(adata.var_names):
         feature_dict[featname] = [i, feat_min[i], feat_max[i]]
 
-    def color_modif(stringval, htlc, rwi, hlw, label_stringval, resize_w, resize_h, bt_slider_range):
+    def color_modif(
+        stringval, htlc, rwi, hlw, label_stringval, resize_w, resize_h, bt_slider_range
+    ):
         stringval_modif = ("  +  " + stringval).replace("  +    -  ", "  -  ").replace(
             "  +    +  ", "  +  "
         ).replace("  +  ", "§§§§§§§§§§  +  ").replace(
@@ -154,12 +156,15 @@ def simple_shrink(s_in, size):
                 select_color_by.value = ""
                 current_style = bt_slider_range.stylesheets[0].css
                 pattern = r"\{margin: 32px 0px 0px -\d+px;\}"
-                new_style = re.sub(pattern,
-                                   "{margin: 32px 0px 0px -" + str(int(legend_width)) + "px;}", current_style)
+                new_style = re.sub(
+                    pattern,
+                    "{margin: 32px 0px 0px -" + str(int(legend_width)) + "px;}",
+                    current_style,
+                )
                 bt_slider_range.stylesheets = [InlineStyleSheet(css=new_style)]
-                bt_slider_range.start = 0.
-                bt_slider_range.end = 1.
-                bt_slider_range.value = (0., 1.)
+                bt_slider_range.start = 0.0
+                bt_slider_range.end = 1.0
+                bt_slider_range.value = (0.0, 1.0)
                 bt_slider_range.step = 0.01
                 bt_slider_range.visible = True
 
@@ -200,7 +205,7 @@ def simple_shrink(s_in, size):
             offset_label.value,  # Include the current label value
             resize_w_input,
             resize_h_input,
-            bt_slider_range
+            bt_slider_range,
         ),
     )
 
@@ -215,7 +220,7 @@ def simple_shrink(s_in, size):
             new_label,  # Pass the new label value to color_modif
             resize_w_input,
             resize_h_input,
-            bt_slider_range
+            bt_slider_range,
         ),
     )
 

diff --git a/yomix/plotting/figure.py b/yomix/plotting/figure.py
@@ -355,7 +355,9 @@ def main_figure(adata, embedding_key, width=900, height=600, title=""):
 
     stylesheet2 = InlineStyleSheet(
         css=".noUi-vertical .noUi-origin {top: 0%;} .noUi-base .noUi-connects "
-        "{height: " + str(height - 55) + "px;} .noUi-target.noUi-vertical {margin: 32px 0px 0px -55px;}"
+        "{height: "
+        + str(height - 55)
+        + "px;} .noUi-target.noUi-vertical {margin: 32px 0px 0px -55px;}"
     )
 
     bt_slider_point_size = bokeh.models.Slider(
@@ -386,14 +388,14 @@ def main_figure(adata, embedding_key, width=900, height=600, title=""):
     bt_slider_range = bokeh.models.RangeSlider(
         start=0.0,
         end=1.0,
-        value=(0., 1.0),
+        value=(0.0, 1.0),
         step=0.01,
         orientation="vertical",
         stylesheets=[stylesheet2],
         width=100,
         show_value=False,
         direction="rtl",
-        visible=False
+        visible=False,
     )
 
     callback_js_slider_range = bokeh.models.CustomJS(
@@ -1397,7 +1399,8 @@ def main_figure(adata, embedding_key, width=900, height=600, title=""):
             args=dict(
                 pbp=points_bokeh_plot,
                 source_rotmatrix_etc=source_rotmatrix_etc,
-                slider_range=bt_slider_range),
+                slider_range=bt_slider_range,
+            ),
             code="""
         var parsed_int = parseInt(this.value);
         if (!isNaN(parsed_int)) {
@@ -1415,12 +1418,13 @@ def main_figure(adata, embedding_key, width=900, height=600, title=""):
     def modif_slider_range(attr, old, new):
         current_style = bt_slider_range.stylesheets[0].css
         pattern = r"\{height: \d+px;\}"
-        new_style = re.sub(pattern, "{height: " + str(max(int(new)-55, 0)) + "px;}", current_style)
+        new_style = re.sub(
+            pattern, "{height: " + str(max(int(new) - 55, 0)) + "px;}", current_style
+        )
         bt_slider_range.stylesheets = [InlineStyleSheet(css=new_style)]
 
     resize_height_input.on_change(
-        "value",
-        lambda attr, old, new: modif_slider_range(attr, old, new)
+        "value", lambda attr, old, new: modif_slider_range(attr, old, new)
     )
 
     sample_search_input = bokeh.models.TextInput(

diff --git a/yomix/plotting/legend.py b/yomix/plotting/legend.py
@@ -7,7 +7,12 @@
 
 
 def setup_legend(
-    pb_plot, obs_string, obs_numerical, source_rotmatrix_etc, resize_width_input, bt_slider_range
+    pb_plot,
+    obs_string,
+    obs_numerical,
+    source_rotmatrix_etc,
+    resize_width_input,
+    bt_slider_range,
 ):
     source = pb_plot.select(dict(name="scatterplot"))[0].data_source
 
@@ -71,7 +76,16 @@ def setup_legend(
     )
 
     def redefine_custom_legend(
-        bokeh_plot, htls, htlc, hlw, obs_col, legend_dict, rwi, obs_s, obs_n, bt_slider_range
+        bokeh_plot,
+        htls,
+        htlc,
+        hlw,
+        obs_col,
+        legend_dict,
+        rwi,
+        obs_s,
+        obs_n,
+        bt_slider_range,
     ):
         if obs_col in obs_s:
             bokeh_plot.right = []
@@ -191,9 +205,7 @@ def all_values(arr) -> np.ndarray:
                 min_val = cbar.ticker.ticks[0]
                 max_val = cbar.ticker.ticks[-1]
                 legend_width = legend_dict[obs_col][1]
-                rwi.value = str(
-                    int(bokeh_plot.width - float(hlw.value) + legend_width)
-                )
+                rwi.value = str(int(bokeh_plot.width - float(hlw.value) + legend_width))
                 hlw.value = str(legend_width)
             else:
                 data = bokeh_plot.select(dict(name="scatterplot"))[0].data_source.data
@@ -238,13 +250,16 @@ def all_values(arr) -> np.ndarray:
                 legend_dict[obs_col] = ([cbar], legend_width)
             current_style = bt_slider_range.stylesheets[0].css
             pattern = r"\{margin: 32px 0px 0px -\d+px;\}"
-            new_style = re.sub(pattern,
-                               "{margin: 32px 0px 0px -" + str(int(legend_width)) + "px;}", current_style)
+            new_style = re.sub(
+                pattern,
+                "{margin: 32px 0px 0px -" + str(int(legend_width)) + "px;}",
+                current_style,
+            )
             bt_slider_range.stylesheets = [InlineStyleSheet(css=new_style)]
             bt_slider_range.start = min_val
             bt_slider_range.end = max_val
             bt_slider_range.value = (min_val, max_val)
-            bt_slider_range.step = (max_val - min_val)/100.
+            bt_slider_range.step = (max_val - min_val) / 100.0
             bt_slider_range.visible = True
 
     hidden_text_label_search = bokeh.models.TextInput(
@@ -347,7 +362,7 @@ def all_values(arr) -> np.ndarray:
             resize_width_input,
             obs_string,
             obs_numerical,
-            bt_slider_range
+            bt_slider_range,
         ),
     )